Supplementary Material

Supplemental Table 1: Clinical characteristics of patients in the study. Patients 1–5 had early relapse/refractory disease; patients 6–10 are long term progression-free.

Supplemental Table 2: List of all 3588 proteins that were identified in the SILAC-based proteomic analysis using LC-MS/MS. 3,027 (84%) of the identified proteins were successfully quantified in at least one of the samples. Identification and quantification in all samples were obtained for 1305 proteins.

Supplemental Table 3: All 87 proteins that were significantly (Student’s t-test, P < 0.05) differentially expressed between the two patient groups. 66 proteins were overexpressed in the group of progression-free patients; 21 proteins were instead overexpressed in the relapsed/refractory group.